Contacts of the helix formed by residues 1137 - 1150 (chain C) in PDB entry 6JBQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU1137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1136C GLN* 1.3 106.9 - - - +
1138C VAL* 1.3 65.9 + - + +
1139C ALA* 3.2 11.1 + - + +
1140C LYS* 3.5 22.9 + - - +
1141C LEU* 3.7 10.4 + - - +
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Residues in contact with VAL1138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136C GLN 5.4 0.9 - - - +
1137C GLU* 1.3 72.7 - - + +
1139C ALA* 1.3 62.5 + - + +
1140C LYS 3.4 0.2 - - - -
1141C LEU* 4.0 8.7 - - + +
1142C ARG* 2.9 37.1 + - - +
1166C ASP* 3.9 35.0 - - - +
1169C VAL* 5.7 6.3 - - + +
1170C MET* 4.2 24.5 - - + -
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Residues in contact with ALA1139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137C GLU* 3.2 8.5 - - + +
1138C VAL* 1.3 83.6 - - + +
1140C LYS* 1.3 63.1 + - + +
1142C ARG* 3.4 10.0 + - - +
1143C GLU* 2.9 29.5 + - - +
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Residues in contact with LYS1140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131C MET* 4.0 7.9 - - - +
1136C GLN* 3.8 36.2 + - + +
1137C GLU* 3.5 11.7 + - - +
1138C VAL 3.4 0.4 - - - -
1139C ALA* 1.3 77.3 - - + +
1141C LEU* 1.3 61.5 + - - +
1143C GLU* 3.4 9.2 + - + +
1144C PHE* 2.9 29.3 + - - +
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Residues in contact with LEU1141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128C ILE* 5.7 3.8 - - + +
1131C MET* 3.8 29.5 - - + +
1132C LEU* 5.1 14.8 - - + -
1136C GLN* 4.9 4.2 - - + +
1137C GLU 3.7 10.4 + - - +
1138C VAL* 3.6 9.5 + - - +
1140C LYS* 1.3 74.3 - - - +
1142C ARG* 1.3 62.7 + - - +
1144C PHE* 3.3 1.6 + - - +
1145C ILE* 2.9 47.3 + - + +
1169C VAL* 4.1 23.8 - - + +
1170C MET* 5.0 16.2 - - + -
1172C LEU* 5.7 0.7 - - + -
1173C ALA* 3.8 33.7 - - + -
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Residues in contact with ARG1142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138C VAL* 2.9 24.0 + - - +
1139C ALA* 3.7 7.8 - - - +
1141C LEU* 1.3 77.2 - - - +
1143C GLU* 1.3 57.8 + - - +
1145C ILE* 3.5 6.2 + - - +
1146C GLN* 2.9 32.1 + - + +
1161C LEU* 2.4 56.2 + - + +
1162C SER* 3.6 18.0 + - - +
1164C PHE* 4.9 6.7 + - - +
1166C ASP* 2.8 42.4 + - - +
1169C VAL* 4.9 13.7 - - + +
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Residues in contact with GLU1143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139C ALA 2.9 17.9 + - - +
1140C LYS* 3.7 11.9 - - + +
1141C LEU 3.3 0.2 - - - -
1142C ARG* 1.3 77.7 - - - +
1144C PHE* 1.3 56.6 + - - +
1146C GLN* 3.4 10.9 + - - +
1147C ARG* 2.9 57.8 + - - +
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Residues in contact with PHE1144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124C ILE* 4.2 27.6 - - + -
1127C LYS* 3.6 38.8 - - + -
1128C ILE* 3.7 26.7 - - + -
1131C MET* 3.7 30.5 - - + -
1140C LYS 2.9 18.5 + - - +
1141C LEU 3.8 0.4 - - - +
1143C GLU* 1.3 75.7 - - - +
1145C ILE* 1.3 65.1 + - + +
1147C ARG* 3.3 15.6 + - + +
1148C ALA* 2.9 29.8 + - + +
1201C LEU* 5.1 19.1 - - + -
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Residues in contact with ILE1145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128C ILE* 4.0 31.6 - - + -
1141C LEU* 2.9 38.0 + - + +
1142C ARG* 4.0 4.0 - - - +
1144C PHE* 1.3 78.8 - - + +
1146C GLN* 1.3 57.3 + - - +
1148C ALA* 3.3 7.5 + - + +
1149C TYR* 2.9 55.5 + - + +
1161C LEU* 3.7 23.3 - - + -
1169C VAL* 6.1 0.7 - - + -
1172C LEU* 4.1 12.3 - - + -
1173C ALA* 6.2 1.8 - - - -
1176C LEU* 4.2 15.3 - - + -
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Residues in contact with GLN1146 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142C ARG* 2.9 20.3 + - + +
1143C GLU* 3.7 15.0 - - - +
1145C ILE* 1.3 77.5 - - - +
1147C ARG* 1.3 56.2 + - + +
1150C ASP* 2.7 69.2 + - - +
1159C VAL 3.7 7.3 + - - -
1160C ASP* 3.2 17.0 + - - +
1161C LEU* 2.8 41.8 + - + +
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Residues in contact with ARG1147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143C GLU* 2.9 45.4 + - - +
1144C PHE* 3.8 15.8 - - + +
1146C GLN* 1.3 77.0 - - + +
1148C ALA* 1.3 61.2 + - - +
1150C ASP* 3.9 8.2 + - - +
1151C LEU* 4.2 11.6 + - - +
1201C LEU* 3.8 35.7 + - + +
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Residues in contact with ALA1148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LYS* 3.9 11.8 - - - -
1124C ILE* 4.7 13.5 - - + -
1144C PHE* 2.9 21.7 + - + +
1145C ILE* 3.8 11.7 - - + +
1146C GLN 3.3 0.2 - - - -
1147C ARG* 1.3 80.6 - - - +
1149C TYR* 1.3 62.4 + - + +
1150C ASP 3.5 0.4 + - - -
1151C LEU* 4.2 9.0 + - - +
1180C MET* 4.3 20.3 - - + +
1198C LEU* 5.5 5.0 - - + +
1201C LEU* 4.2 19.3 - - + +
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Residues in contact with TYR1149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.2 46.8 + - + +
13C LYS* 3.6 40.3 + - + +
1145C ILE* 2.9 41.3 + - + +
1146C GLN* 4.8 0.9 - - - -
1147C ARG 3.4 0.2 - - - -
1148C ALA* 1.3 80.9 - - + +
1150C ASP* 1.3 67.0 + - - +
1151C LEU 3.4 5.2 + - - -
1155C VAL* 4.9 7.8 - - - +
1157C GLN* 5.5 2.9 - - + +
1158C LYS* 5.6 1.6 + - - -
1159C VAL* 4.0 29.6 + - + +
1161C LEU* 4.0 10.1 - - + -
1172C LEU* 5.1 2.5 - - + -
1176C LEU* 3.4 22.9 - - + +
1180C MET* 3.7 22.6 - - + +
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Residues in contact with ASP1150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146C GLN* 2.7 48.5 + - - +
1147C ARG* 3.9 6.9 + - - +
1148C ALA 3.5 0.6 - - - -
1149C TYR* 1.3 85.2 - - - +
1151C LEU* 1.3 64.3 + - - +
1152C GLY* 3.6 2.1 + - - -
1158C LYS* 5.8 2.6 + - - -
1159C VAL 3.4 14.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il